You're focusing on the details of my examples too much. In
our universe, you cannot create a system of any kind unaffected by the world around it, this is a fundamental law. No system you build can be entirely isolated from the world around it. You can isolate it in this way or that way, but you cannot entirely prevent interaction with the outside world. A computer is not some magical foam that insulates software running on it from the universe if the programmer so desires. If you run a program where some entity inside is even capable of investigating that it is just inside a program, there will be indicators, period. That is in our universe. It doesn't matter if it is a computer or some other method of running the simulation, from inside, there will be detectable effects to any entity that tries to investigate enough.
In a universe where this is not true, that is, systems can emerge that are entirely isolated from the rest of it, even so far as not having to obey the physical laws of said universe, that would be the stable state of emergent systems within that universe. Systems generally would not interact with one another. So even if an entity in that universe could construct a simulation of some kind, and the universe around it had no impact on it whatsoever, it would not be able to observe the simulation and so it would be either pointless or not a simulation at all which both amount to the same thing.
I should note, I'm not saying that we aren't in one, I don't think we are but if we are, it is fundamentally falsifiable and if the more we understand our universe we see no indication of it, that means we aren't in one.